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- PDB-6om1: Crystal structure of an atypical integrin -

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Basic information

Entry
Database: PDB / ID: 6om1
TitleCrystal structure of an atypical integrin
Components
  • Integrin alpha-V
  • Integrin beta-8
KeywordsIMMUNE SYSTEM / Integrin / TGF-beta activation
Function / homology
Function and homology information


ganglioside metabolic process / hard palate development / Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding ...ganglioside metabolic process / hard palate development / Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / placenta blood vessel development / Laminin interactions / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / regulation of phagocytosis / : / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / cartilage development / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / microvillus membrane / cell-substrate adhesion / positive regulation of osteoblast proliferation / endodermal cell differentiation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / positive regulation of intracellular signal transduction / lamellipodium membrane / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / voltage-gated calcium channel activity / vasculogenesis / specific granule membrane / coreceptor activity / extrinsic apoptotic signaling pathway in absence of ligand / phagocytic vesicle / ERK1 and ERK2 cascade / positive regulation of cell adhesion / transforming growth factor beta receptor signaling pathway / substrate adhesion-dependent cell spreading / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / calcium ion transmembrane transport / cell-cell adhesion / response to virus / VEGFA-VEGFR2 Pathway / ruffle membrane / positive regulation of angiogenesis / integrin binding / cell migration / virus receptor activity / positive regulation of cytosolic calcium ion concentration / protease binding / angiogenesis / cell adhesion / immune response / positive regulation of cell migration / symbiont entry into host cell / external side of plasma membrane / negative regulation of gene expression / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / cell surface / extracellular exosome / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Integrin domains. Chain A, domain 2 / Integrin alpha, N-terminal / Teneurin-like EGF domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit ...Integrin domains. Chain A, domain 2 / Integrin alpha, N-terminal / Teneurin-like EGF domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin alpha-V / Integrin beta-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsWang, J.C. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)NIH grant AR-067288 United States
CitationJournal: Nat Commun / Year: 2019
Title: General structural features that regulate integrin affinity revealed by atypical alpha V beta 8.
Authors: Wang, J. / Su, Y. / Iacob, R.E. / Engen, J.R. / Springer, T.A.
History
DepositionApr 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-V
B: Integrin beta-8
C: Integrin alpha-V
D: Integrin beta-8
E: Integrin alpha-V
F: Integrin beta-8
G: Integrin alpha-V
H: Integrin beta-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,64886
Polymers465,6018
Non-polymers23,04778
Water7,764431
1
A: Integrin alpha-V
B: Integrin beta-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,52721
Polymers116,4002
Non-polymers6,12719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint62 kcal/mol
Surface area42710 Å2
MethodPISA
2
C: Integrin alpha-V
D: Integrin beta-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,95921
Polymers116,4002
Non-polymers5,55919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10770 Å2
ΔGint52 kcal/mol
Surface area40740 Å2
MethodPISA
3
E: Integrin alpha-V
F: Integrin beta-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,99721
Polymers116,4002
Non-polymers5,59719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint54 kcal/mol
Surface area40950 Å2
MethodPISA
4
G: Integrin alpha-V
H: Integrin beta-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,16523
Polymers116,4002
Non-polymers5,76521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint64 kcal/mol
Surface area42120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.240, 55.070, 175.070
Angle α, β, γ (deg.)90.37, 107.00, 90.01
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Integrin alpha-V / Vitronectin receptor / Vitronectin receptor subunit alpha


Mass: 65738.719 Da / Num. of mol.: 4 / Mutation: M400GC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA, VTNR / Plasmid: pcDNA3.1 / Details (production host): Hygromycin resistance / Cell line (production host): HEK293s Gnt1 -/- / Production host: Homo sapiens (human) / Strain (production host): HEK293 / References: UniProt: P06756
#2: Protein
Integrin beta-8


Mass: 50661.445 Da / Num. of mol.: 4 / Mutation: V301C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB8 / Production host: Homo sapiens (human) / References: UniProt: P26012

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Sugars , 8 types, 37 molecules

#3: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 472 molecules

#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#12: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#13: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#14: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 100 mM MES, pH 6.7, 12% PEG 20000 / PH range: 6.3 - 6.7

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.66→48.072 Å / Num. obs: 141394 / % possible obs: 95.5 % / Redundancy: 1.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.133 / Net I/σ(I): 5.87
Reflection shellResolution: 2.66→2.73 Å / Redundancy: 1.7 % / Num. unique obs: 10550 / CC1/2: 0.199 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UM9

4um9


Resolution: 2.66→48.072 Å / Cross valid method: FREE R-VALUE / σ(F): 3.18 / Phase error: 39.34
RfactorNum. reflection% reflection
Rfree0.2796 1964 1.39 %
Rwork0.2477 --
obs0.2486 141394 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.66→48.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29839 0 318 431 30588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00330864
X-RAY DIFFRACTIONf_angle_d0.73641945
X-RAY DIFFRACTIONf_dihedral_angle_d14.04818420
X-RAY DIFFRACTIONf_chiral_restr0.0454873
X-RAY DIFFRACTIONf_plane_restr0.0035291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6601-2.7320.47721450.427410853X-RAY DIFFRACTION96
2.732-2.81240.41631440.406410898X-RAY DIFFRACTION96
2.8124-2.90310.33991450.376610983X-RAY DIFFRACTION96
2.9031-3.00690.38031460.349410798X-RAY DIFFRACTION96
3.0069-3.12720.36791420.327910911X-RAY DIFFRACTION96
3.1272-3.26950.36921440.31410839X-RAY DIFFRACTION95
3.2695-3.44170.32211460.295410774X-RAY DIFFRACTION94
3.4417-3.65720.33781430.279410490X-RAY DIFFRACTION92
3.6572-3.93940.28311430.253210467X-RAY DIFFRACTION92
3.9394-4.33540.24851400.221110444X-RAY DIFFRACTION92
4.3354-4.96180.23251420.190510657X-RAY DIFFRACTION93
4.9618-6.24750.23451460.20910699X-RAY DIFFRACTION94
6.2475-40.05120.24441480.213110670X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3987-0.28560.48561.9728-0.08673.11020.09970.0126-0.06130.2599-0.0107-0.06890.32130.0531-0.11340.6861-0.0699-0.24080.57-0.06560.4731-21.8895-15.35274.9324
24.3573-0.12333.01691.717-0.09824.76830.3317-0.2546-0.3571-0.31610.31050.52040.5275-1.0258-0.63521.286-0.1042-0.49511.06370.0590.8227-43.0864-26.3445-41.0364
37.1053-0.6188-0.84418.2616-0.20862.0791-0.7534-0.11240.5853-0.58570.28390.6097-0.2684-0.37510.51921.17530.064-0.26241.68530.08531.1432-65.32092.98844.6402
42.6946-1.0399-1.19883.1641-0.76531.5083-0.2088-0.85090.42871.11850.15170.0496-0.0316-0.38790.05541.081-0.0551-0.13721.1187-0.20520.5979-45.354-2.712127.3338
52.2778-0.27251.05161.8227-0.53522.68490.01780.08-0.054-0.11760.0471-0.1630.03650.0616-0.05460.8011-0.1043-0.23160.5356-0.10990.4795-0.652110.0976-34.7026
61.7714-0.46772.62320.2202-0.57154.706-0.5190.58850.2479-0.79970.50860.3732-0.5335-0.03690.06381.8149-0.4408-0.6551.32530.0690.9076-29.556923.2248-76.6841
74.36810.728-2.81085.67810.69552.1557-0.67750.4096-0.2251-0.8470.68390.21090.95210.6879-0.0331.78790.0126-0.14681.7192-0.4321.41520.5532-10.9115-70.2847
85.4567-0.6688-1.65546.33860.28962.8733-0.10360.0813-0.49240.14450.064-1.17850.61721.20810.04950.84370.1549-0.17941.0703-0.17290.868429.598-4.5783-43.3059
92.36590.35851.66072.20450.25944.65460.2487-0.56960.06720.1133-0.20470.02390.5315-0.7561-0.0190.8897-0.0747-0.32560.8309-0.17280.647231.13973.932623.7781
101.03040.43630.76821.4644-0.50192.76490.17340.9009-1.38560.03520.7694-0.81480.19441.1658-0.94011.809-0.161-0.63061.4657-0.47071.32153.8689-7.939269.5724
112.5412-1.745-0.95152.9423-0.26020.8359-0.5376-0.43650.98610.64610.4218-0.656-0.05950.1510.17021.3211-0.2804-0.40951.6738-0.45551.725569.035330.054628.9808
125.49892.078-2.69576.7174-0.34733.44330.09090.42950.7288-0.8863-0.14390.0648-0.23230.21120.04920.82460.0859-0.24190.711-0.04060.727852.031123.67714.0847
132.26080.22861.20831.70850.39581.7922-0.38940.1382-0.02740.13390.01930.1271-0.64490.307-0.17291.50640.0045-0.53430.7707-0.12320.523110.5996-10.668663.3386
141.63670.25131.52150.6331-0.1491.6559-0.7089-0.48410.34570.21410.403-0.062-0.7815-0.16460.01712.21880.2461-0.821.3008-0.20231.005737.82411.9679106.9685
151.21350.0634-0.93215.39841.01651.068-0.3545-0.3568-0.10150.93460.4748-0.10580.56110.2607-0.1271.89920.32720.12161.80710.27621.4615-5.1568-37.446997.8647
164.2790.881-1.80896.4086-2.54073.4687-0.27170.1034-0.3895-0.21480.11791.09690.0305-0.67590.14940.98590.1696-0.24740.8593-0.28441.0735-17.4294-30.10569.8659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:438 )A1 - 438
2X-RAY DIFFRACTION2( CHAIN A AND RESID 439:594 )A439 - 594
3X-RAY DIFFRACTION3( CHAIN B AND ( RESID 66:101 OR RESID 345:420 ) )B66 - 101
4X-RAY DIFFRACTION3( CHAIN B AND ( RESID 66:101 OR RESID 345:420 ) )B345 - 420
5X-RAY DIFFRACTION4( CHAIN B AND RESID 102:344 )B102 - 344
6X-RAY DIFFRACTION5( CHAIN C AND RESID 1:438 )C1 - 438
7X-RAY DIFFRACTION6( CHAIN C AND RESID 439:594 )C439 - 594
8X-RAY DIFFRACTION7( CHAIN D AND ( RESID 73:101 OR RESID 345:419 ) )D73 - 101
9X-RAY DIFFRACTION7( CHAIN D AND ( RESID 73:101 OR RESID 345:419 ) )D345 - 419
10X-RAY DIFFRACTION8( CHAIN D AND RESID 102:344 )D102 - 344
11X-RAY DIFFRACTION9( CHAIN E AND RESID 1:438 )E1 - 438
12X-RAY DIFFRACTION10( CHAIN E AND RESID 439:594 )E439 - 594
13X-RAY DIFFRACTION11( CHAIN F AND ( RESID 73:101 OR RESID 345:422 ) )F73 - 101
14X-RAY DIFFRACTION11( CHAIN F AND ( RESID 73:101 OR RESID 345:422 ) )F345 - 422
15X-RAY DIFFRACTION12( CHAIN F AND RESID 102:344 )F102 - 344
16X-RAY DIFFRACTION13( CHAIN G AND RESID 1:438 )G1 - 438
17X-RAY DIFFRACTION14( CHAIN G AND RESID 439:594 )G439 - 594
18X-RAY DIFFRACTION15( CHAIN H AND ( RESID 73:101 OR RESID 345:422 ) )H73 - 101
19X-RAY DIFFRACTION15( CHAIN H AND ( RESID 73:101 OR RESID 345:422 ) )H345 - 422
20X-RAY DIFFRACTION16( CHAIN H AND RESID 102:344 )H102 - 344

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